The yellow fever mosquito, Aedes aegypti, is the main vector of the most important arthropod-borne viral diseases affecting humans, namely yellow fever and dengue fever. Efficient vector control programs and informative epidemiological studies, which are essential for the control of these diseases, requires a better understanding of the genetic variations within and between Ae. aegypti vector populations. The objective of this proposed research is to develop a novel approach to analyze the genetic variations in Ae. aegypti populations, which offers several significant advantages and complements existing methods. Our approach is based on recently demonstrated insertion polymorphism of a family of highly reiterated short interspersed repetitive elements (SINEs) named Feilai in Ae. aegypti (Tu, 1999, Mol. Biol. Evol. 16:760-772). Here we propose to develop a systematic approach to isolate these polymorphic Feilai insertion markers. Like the Alu insertion markers in humans (e.g., de Pancorbo et al., 2001, Hum. Genet. 109:224-233; Roy-Engel et al., 2001, Genetics 159:279-290). Feilai markers can offer several major advantages including the ability to distinguish between ancestral and derived states of the two alleles, the extreme ease of use, and the potential for high-throughput assays. During this R03 pilot project, we will pursue the following Specific Aims: 1) Develop a high-throughput assay for the co-dominant FIP markers; 2) Construct a more detailed phylogenetic framework, to classify Ae. aegypti Feilai subfamilies; 3) Develop different approaches to systematically isolate co-dominant FIP markers, with the focus on representative sampling and direct testing of different Feilai subfamilies and/or groups. The future goals extending beyond this proposed R03 pilot project are to isolate a large number of high-throughput Feilai insertion polymorphism markers, and to use these powerful markers to study the genetic variability and the genetic basis of vectorial competence of Ae. aegypti in natural populations.